I experimented with ebony pins replacing plastic on a nice Martin many years ago, and found no difference in tone. The ebony simply looked nicer.

Back then, even 40 series Martins came with plastic pins with little fake inlays in them!

Claims have been made for many years about brass or mammoth ivory pins, but I haven't tried them.

i think strings will make a more noticeable difference, but agree that wooden pins look nicer than plastic. Then again, a lot of nice features come with those SEs, cost savings had to be found where they could no doubt!

I recently purchased a PRS Angelus SE A30 and noticed the plastic bridge pins. Wanting to replace them with boxwood or ebony pins I purchased a set of each from DiAddario and to my shagrin neither fit very well at all. Apparently the diameter of the stock bridge pins is 5mm (according to PRS customer service) which are a bit difficult to find. Just as an SOP when I get a new guitar, I do a restring and if switch to ebony, boxwood, ivory or tusq bridge pins, (just my preference) and I have found over the years that the quality of the pins does make a tonal difference as more of the vibration of the strings is transferred into the body, whereas with lesser pins, air bubbles or other voids tend to dampen the vibration transfer. IMHO of course